Chromosome instability (CIN) is a hallmark of cancers and may contribute to tumorigenesis. Many genes involved in maintaining chromosome stability are conserved in eukaryotes, and some are mutated in cancers. The goal of this thesis is to use Saccharomyces cerevisiae as a model to identify and characterize genes important for chromosome maintenance, investigate the relevance of CIN to cancer, and develop a strategy to identify candidate therapeutic target genes for selective killing of cancer cells. To systematically identify genes important for chromosome stability, nonessential gene deletion yeast mutants were examined using 3 complementary CIN assays. The chromosome transmission fidelity assay monitors loss of an artificial chromosome. The bimater assay monitors loss of heterozygosity at the mating type locus in homozygous diploid deletion mutants. The a-like faker assay detects loss of the MATα mating type locus in haploid deletion mutants. 293 CIN mutants were identified, including genes functioning in the chromosome or cell cycle, and genes not clearly implicated in chromosome maintenance, such as MMS22, MMS1, RTT101 and RTT107. Phenotypic, genetic and biochemical analyses of these 4 gene products indicate that they function in double strand break repair. They may form a ubiquitin ligase complex that regulates the level of some proteins, including Mms22p itself, during DNA damage response. Human homologues of 10 yeast CIN genes identified were previously shown to be mutated in cancers, suggesting that other human homologues are candidate cancer genes. 101 human homologues of yeast CIN genes were sequenced in a panel of colorectal cancers, identifying 20 somatic mutations in 8 genes. In particular, 17 mutations were found in 5 genes involved in sister chromatid cohesion. Further functional studies should reveal whether mutations in cohesion genes contribute to CIN in cancers. While CIN mutations may contribute to cancer, CIN cancer cells may become inviable when combined with another non-essential mutation, providing the basis for cancer cell-specific therapy. Mutations in CTF4, CTF18, and DCC1 in yeast cause synthetic lethality when combined with mutations in various CIN genes whose human homologues are mutated in cancers. Such analyses in yeast can propose potential drug targets in human for cancer therapy.